| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:24 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the COMPASS package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 385/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| COMPASS 1.37.0 (landing page) Greg Finak
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: COMPASS |
| Version: 1.37.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:COMPASS.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings COMPASS_1.37.0.tar.gz |
| StartedAt: 2022-12-28 22:43:23 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 22:45:29 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 125.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COMPASS.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:COMPASS.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings COMPASS_1.37.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/COMPASS.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'COMPASS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'COMPASS' version '1.37.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'COMPASS' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'BiocStyle' 'foreach' 'rmarkdown'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.CellCounts: no visible binding for global variable
'_COMPASS_CellCounts'
COMPASSfitToCountsTable: no visible binding for global variable
'population'
COMPASSfitToCountsTable: no visible binding for global variable 'Count'
COMPASSfitToCountsTable: no visible binding for global variable 'id'
CellCounts_character: no visible binding for global variable
'_COMPASS_CellCounts_character'
GetThresholdedIntensities : <anonymous>: no visible global function
definition for 'gh_pop_is_bool_gate'
Undefined global functions or variables:
Count _COMPASS_CellCounts _COMPASS_CellCounts_character
gh_pop_is_bool_gate id population
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/COMPASS/libs/x64/COMPASS.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'test-all.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/COMPASS.Rcheck/00check.log'
for details.
COMPASS.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL COMPASS
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'COMPASS' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c COMPASS_init.c -o COMPASS_init.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CellCounts.cpp -o CellCounts.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CellCounts_character.cpp -o CellCounts_character.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c digamma.c -o digamma.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mat2vec.c -o mat2vec.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c melt_dataframe.c -o melt_dataframe.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c melt_matrix.c -o melt_matrix.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c samplePuPs.cpp -o samplePuPs.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c transpose_list.c -o transpose_list.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updatealphas_Exp.cpp -o updatealphas_Exp.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updatealphas_Exp_MH.cpp -o updatealphas_Exp_MH.o
updatealphas_Exp_MH.cpp: In function 'SEXPREC* updatealphas_Exp_MH(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
updatealphas_Exp_MH.cpp:26:10: warning: variable 'psik' set but not used [-Wunused-but-set-variable]
26 | double psik = 0.;
| ^~~~
updatealphas_Exp_MH.cpp:35:7: warning: variable 'flagkk' set but not used [-Wunused-but-set-variable]
35 | int flagkk = 0;
| ^~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updatealphau.cpp -o updatealphau.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updatealphau_noPu_Exp_MH.cpp -o updatealphau_noPu_Exp_MH.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updatebeta_RW.cpp -o updatebeta_RW.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updategammak_noPu.cpp -o updategammak_noPu.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
g++ -std=gnu++11 -shared -s -static-libgcc -o COMPASS.dll tmp.def COMPASS_init.o CellCounts.o CellCounts_character.o RcppExports.o digamma.o mat2vec.o melt_dataframe.o melt_matrix.o samplePuPs.o transpose_list.o updatealphas_Exp.o updatealphas_Exp_MH.o updatealphau.o updatealphau_noPu_Exp.o updatealphau_noPu_Exp_MH.o updatebeta_RW.o updategammak_noPu.o utils.o -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-COMPASS/00new/COMPASS/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (COMPASS)
COMPASS.Rcheck/tests/test-all.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(COMPASS)
> library(flowWorkspace)
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:
vignette("flowWorkspace-Introduction", "flowWorkspace")
> if (file.exists("testthat")) {
+ test_dir("testthat")
+ }
✔ | F W S OK | Context
⠏ | 0 | COMPASS
⠏ | 0 | COMPASS Interface
⠋ | 1 | COMPASS Interface
✔ | 1 | COMPASS Interface [0.6s]
⠏ | 0 | COMPASSPlot
⠏ | 0 | test plotCOMPASSResultStack
⠋ | 1 | test plotCOMPASSResultStack
⠹ | 3 | test plotCOMPASSResultStack
✔ | 6 | test plotCOMPASSResultStack [42.1s]
⠏ | 0 | CellCounts
⠏ | 0 | CellCounts
✔ | 7 | CellCounts
⠏ | 0 | FunctionalityScore
⠏ | 0 | FS, PFS
✔ | 8 | FS, PFS
⠏ | 0 | GatingSet2COMPASS
⠏ | 0 | test COMPASSContainerFromGatingSet
⠋ | 1 0 | test COMPASSContainerFromGatingSet
⠴ | 2 4 | test COMPASSContainerFromGatingSet
✔ | 2 7 | test COMPASSContainerFromGatingSet [0.5s]
────────────────────────────────────────────────────────────────────────────────
Warning ('test-GatingSet2COMPASS.R:15'): COMPASSContainerFromGatingSet
There appear to be negative intensities in the 'data' supplied.
Backtrace:
1. COMPASS::COMPASSContainerFromGatingSet(...)
at test-GatingSet2COMPASS.R:15:2
2. COMPASS::COMPASSContainer(...)
Warning ('test-GatingSet2COMPASS.R:30'): COMPASSContainerFromGatingSet
There appear to be negative intensities in the 'data' supplied.
Backtrace:
1. COMPASS::COMPASSContainerFromGatingSet(...)
at test-GatingSet2COMPASS.R:30:2
2. COMPASS::COMPASSContainer(...)
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 43.4 s
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 29 ]
>
> proc.time()
user system elapsed
45.89 1.07 46.93
COMPASS.Rcheck/COMPASS-Ex.timings
| name | user | system | elapsed | |
| COMPASS | 0.26 | 0.02 | 0.28 | |
| COMPASSContainer | 0.03 | 0.00 | 0.03 | |
| COMPASSContainerFromGatingSet | 0 | 0 | 0 | |
| CellCounts | 0.28 | 0.05 | 0.31 | |
| Combinations | 0.02 | 0.00 | 0.01 | |
| FunctionalityScore | 0 | 0 | 0 | |
| GetThresholdedIntensities | 3.30 | 0.33 | 3.96 | |
| PolyfunctionalityScore | 0 | 0 | 0 | |
| Posterior | 0.00 | 0.01 | 0.01 | |
| Response | 0 | 0 | 0 | |
| SimpleCOMPASS | 2.01 | 0.05 | 2.07 | |
| TotalCellCounts | 0.02 | 0.00 | 0.01 | |
| UniqueCombinations | 0.01 | 0.00 | 0.02 | |
| getCounts | 0.03 | 0.00 | 0.03 | |
| merge.COMPASSContainer | 0 | 0 | 0 | |
| pheatmap | 0.68 | 0.02 | 0.69 | |
| plot.COMPASSResult | 0.03 | 0.00 | 0.03 | |
| plotCOMPASSResultStack | 0 | 0 | 0 | |
| print.COMPASSContainer | 0 | 0 | 0 | |
| print.COMPASSResult | 0 | 0 | 0 | |
| scores | 0 | 0 | 0 | |
| select_compass_pops | 0 | 0 | 0 | |
| shinyCOMPASS | 0 | 0 | 0 | |
| shinyCOMPASSDeps | 1.67 | 0.91 | 2.58 | |
| subset.COMPASSContainer | 0 | 0 | 0 | |
| summary.COMPASSContainer | 0 | 0 | 0 | |
| summary.COMPASSResult | 0 | 0 | 0 | |
| translate_marker_names | 0 | 0 | 0 | |
| transpose_list | 0 | 0 | 0 | |